The whole reason that happened was because Pharaoh was not letting the Israelite slaves leave Egypt and worship God, so that they can venture out to the promised land. God gave everyone the choice to keep their sons alive by doing specific tasks. In other words, they had the choice to avoid their sons dying. And nobody is considered innocent. EVERYONE has sinned, so saying God killed innocent people is not true.
On the other hand, God IS the ruler of the universe. This gives him authority to make decisions which ordinary human beings are not allowed to make. Just like an earthly Governor or Judge has authority to do some things which ordinary citizens don't have the right to do, God has the authority to do anything, i.e. any type of act. For example, everything belongs to God, so when he takes things from us it is not stealing, but doing what he likes with his own property. Similarly, if God kills people it is not murder, because our lives belong to him.
Note that, as the ruler of the universe God actually kills everyone. All people are mortal, some of them die young, and God is responsible for this state of affairs. Sometimes he does it miraculously in order to make a special point, but more often it he causes it to happen naturally. Before I ask whether I can trust a God who killed the Canaanite children, I first need to ask whether I can trust a God who will kill ME. As Christians, we trust that God is using death as a tool in order to turn us into the people he wants us to become. Partly, we trust him because he came to Earth and died for us, so he isn't asking us to suffer anything which he hasn't gone through himself.